I mean it in the following way: How did they justify going to war with other Christian nations at all? War is a very bad thing. So usually there is felt to be a need for an 'official' compelling justification for going to war. Also, back then European States must have thought it was important for war to be consistent with Christianity. And yet, Christianity seems to me the sort of religion that makes war a difficult thing to justify, especially among Christian nations. So how did they justify war at all? Under what conditions was it considered acceptable? What was the Church's position on this?
/u/verificationist
I think you'll get much better answers if you make your question more specific. In that era, many wars were fought over many reasons, with different justifications. Dynastic claims were a major rationale for war, as was religious. It depends on who and what you are talking about.
I am not aware of a comprehensive survey of every war and the justification of each of them, unfortunately.
Do you have any specific conflicts in mind?
In that era, mainstream Christanity did not generally espouse pacifism and condemn violence. Only specific people and groups did, such as the Ultraquists, the Anabaptists, Erasmus.
Further, the church was nowhere near a centralized monolithic entity. Isabella and Ferdinand were able to control bishop appointments in their realms, thus effectively they controlled those positions. Similarly in France, and to varying extent in Germany and the various bishoprics in Italy. As a result, it was easy for monarchs to manipulate their local church into supporting them.
As far as the ethical justification goes, dynastic claims were a major cause for war. The Italian wars were fought over the dynastic claims of the Angevin to the throne of Naples, and this claim was inherited through a succession of French kings all the way to Francis I. Ferdinand II Aragon fought against the French in support of the reigning monarchs, of the Neapolitan branch of the House of Trastamara of Spain. Eventually, he usurped the throne himself using this family claim.
Obviously, religion is another justification, I won't go through it here because there are countless examples in the various Wars of Religion.
The rights of kings and nobles is another reason, for example Charles V's pacification of Ghent in 1547 was due to Ghent's refusal to pay their due taxes and their attempt to court the French king to protect them. Conversely, the German Peasants War in the 1520s broke out due to perceived injustices by kings and nobles.
For a perspective on the small but growing pacifist movement, check out The Reformation by MacCulloch.